Enhanced production of polyhydroxybutyrate by multiple dividing E. coli

Background Most bacteria are grown in a binary fission way meaning a bacterial cell is equally divided into two. Polyhydroxyalkanoates (PHA) can be accumulated as inclusion bodies by bacteria. The cell division way and morphology have been shown to play an important role in regulating the bacterial growth and PHA storages. Results The common growth pattern of Escherichia coli was changed to multiple fission patterns by deleting fission related genes minC and minD together, allowing the formation of multiple fission rings (Z-rings) in several positions of an elongated cell, thus a bacterial cell was observed to be divided into more than two daughter cells at same time. To further improve cell growth and PHA production, some genes related with division process including ftsQ, ftsL, ftsW, ftsN and ftsZ, together with the cell shape control gene mreB, were all overexpressed in E. coli JM109 ∆minCD. The changing pattern of E. coli cell growth and morphology resulted in more cell dry weights (CDW) and more than 80 % polyhydroxybutyrate (PHB) accumulation increases compared to its binary fission control grown under the same conditions. Conclusions This study clearly demonstrated that combined over-expression genes ftsQ, ftsW, ftsN, ftsL and ftsZ together with shape control gene mreB in multiple division bacterial E. coli JM109 ∆minCD benefited PHA accumulation. Our study provides useful information on increasing the yield of PHA by changing the cell division pattern and cell morphology of E. coli. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0531-6) contains supplementary material, which is available to authorized users.


Background
In Escherichia coli, cell division is regulated strictly to ensure that daughter cells contain proper cellular components [1]. Most bacteria are divided via binary fission, allowing a parent cell to split in two [2]. During this process, several genes and their products are important, such as the tubulin-like protein FtsZ [3], and MinC, MinD and MinE that regulate the formations of division sites [4,5]. The MinC and MinD are inhibitors able to block the formation of the FtsZ ring at all sites, while MinE relieves the division block at the mid-cell site, resulting in binary fission [4,6]. In the absence of MinC and MinD, the divisions appear to form at all division sites since FtsZ rings can be generated at both polar and medial positions [7,8]. On the other hand, deletion of the 'min' system results in the production of some mini-cells, products of divisions near the E. coli cell poles [9]. The cell division pattern could be changed by disrupting the 'min' system, allowing the common binary fission be changed to multiple fissions [10].
To change the replication process of a bacterial cell, the formation of FtsZ ring and proper septation should be manipulated [6]. There are at least ten genes that have been shown to be essential for formation of the FtsZ ring and regulation the division process [11,12]. Among the essential genes, FtsQ and FtsL are two membrane proteins localizing to the cell septum during division process [13,14], and the location of FtsW is dependent on the prior localization of FtsQ and FtsL [15,16]. As the last protein acted in cell division, FtsN causes the disassembly of other elements from the division ring [17,18]. FtsZ interacts with FtsQ, FtsL, FtsW and FtsN in the progression and completion of cytokinesis [12]. FtsZ also plays an important role in the bacterial cell division process as a tubulin-like protein [12,19,20].
Polyhydroxyalkanoates (PHA), a family of biodegradable and biocompatible thermal polyesters or bioplastics, are accumulated as inclusion bodies by bacteria under unbalanced growth conditions [21][22][23]. Polyhydroxybutyrate (PHB) is the model PHA used for many demonstration studies, and it has been developed as environmentally friendly bioplastics with promising applications [24,25]. High cost of PHA production has been a key limiting factor on its commercial application [26]. Efforts on process optimization, use of cheap carbon sources and pathway engineering were made to cut cost [27][28][29][30][31]. Although the cost of PHA production can be reduced under these efforts, it is still significantly higher compared with the petrochemical plastics such as polyethylene (PE) [24]. Therefore, other methods are needed to reduce the cost of PHA [32,33].
Since PHA are produced by bacteria as inclusion bodies, cell shapes of the host strain can affect the amount of PHA granules and the quantity of PHA that can be stored [34,35]. The change of cell division process could produce more daughter cells in various shapes at the same time, possibly leading to more PHA, as was indicated by previous studies that PHA synthesis is also limited by the small cell size, a large cell size with more space can allow more PHA granules to be accumulated. Bacterial peptidoglycan cell wall and the actin-like protein MreB cytoskeleton are major determinants of cell shape in rodshaped bacteria such as E. coli [36][37][38].
In this study, we aimed to change the cell division pattern and thus cell morphology, and to use the multiple fission cells for possible enhanced PHB accumulation.

Changing E. coli growth pattern: from binary division to multiple fission
In this study, genes minC and minD regulating fission ring locations were deleted in E. coli JM109 using homologous recombination method. E. coli JM109 ∆minCD became several folds longer than the wild type when cultivated in LB medium (Fig. 1), sizes extended from 1-3 μm for the wild type (Fig. 1a) to around 5 μm for the E. coli JM109 ∆minCD (Fig. 1d), accompanied by some mini-cells attached around the elongated cells. Interestingly, the individual mutant of minC and minD in E. coli JM109, respectively, namely, E. coli JM109 ∆minC (Fig. 1b) and E. coli JM109 ∆minD (Fig. 1c), displayed a similar morphology to E. coli JM109 ∆minCD (Fig. 1d).
The reason may be attributed to joint efforts of minC and minD to decide FtsZ ring formation [7]. Both are essential for the function of 'min' system.
In the absences of minC and/or minD, the FtsZ ring fails to locate to the middle of a cell ( Fig. 2a; Additional file 1: Video S1). Under this circumstance, E. coli JM109 ∆minCD changes not only the cell morphology ( Fig. 1) but also the way of cell division (Fig. 2a). As multiple FtsZ rings were randomly and simultaneously formed in various positions of an elongated cell of E. coli JM109 ∆minCD, one elongated bacterial cell was broken into more than two daughter cells (Additional file 1: Video S1). For example, a cell of an elongated E. coli JM109 ∆minCD was divided into three daughter cells when two FtsZ rings were formed and located in two different positions of the elongated cell. The size of the daughter cell is dependent on the position where the FtsZ ring is formed. Some mini-cells were observed during the multiple fission process when the FtsZ ring was formed at a polar site where no nucleic acid was available for encapsulating into the cellular space (Fig. 2a). E. coli JM109 ∆minCD changes not only its cell size but also its way of growth.
Growth rate from the binary division to multiple fission was investigated in terms of the OD 600 and cell dry weight (CDW) of the wild type and mutant grown in LB medium for 24 h, respectively. Even though OD 600 of E. coli JM109 ∆minCD showed a little bit higher than that of the wild type (Fig. 2b), the cell dry weights indicated only little significant difference between the mutant and wild type (Fig. 2c). OD values were not only related to cell density but also to the cell morphology. Thus, the mutant strain could achieve higher OD value since the cell length was changed. However, the cell dry weight was not enhanced, the reason could be attributed to the mini-cells that could not make a contribution to the final CDW.
When E. coli JM109∆minCD was used to express PHB synthesis operon phbCAB encoded by plasmid pBHR68, it was found that the mutant accumulated slightly more PHB compared with its wild type under the same conditions. When grown in a mineral medium supplemented with yeast extract, the amount of PHB produced by E. coli JM109 ∆minCD had a little increase compared with the wild type E. coli JM109. However, the different amounts of yeast extract added into the MM medium (mineral or minimal growth medium) had little effect on the enhancements on cell growth and PHB accumulation (Table 1). When E. coli JM109∆minCD was cultured in MM medium containing 1 g/L yeast extract, the cell dry weight was 5.12 g/L and PHB contents was 43.08 %, which was higher than the control one and other culture conditions in MM medium. On the other hand, when the mutant was cultivated in LB medium for 48 h, the cell dry weight could reach 8.35 g/L containing 60.23 % PHB, much higher than the control E. coli JM109 having only 53.22 % PHB (Fig. 2d). In all cases, LB medium supported better cell growth and PHB synthesis compared with the mineral medium added with yeast extracts (Table 1; Fig. 2d). Since the LB medium was more suitable for E. coli JM109∆minCD, subsequent study was employed only the LB medium. It was concluded that multiple fission promoted the PHB accumulation compared to the common binary fission way of growth when cultivations were conducted in LB medium.

FtsZ, overexpression in E. coli JM109∆minCD led to multiple dividing cells accumulating more PHB
As an essential cell division protein, FtsZ forms a contractile ring structure (FtsZ ring) at the cell division site, regulation of FtsZ ring assembly controls the timing and the location of cell division [39,40]. FtsZ ring formed by FtsZ assembly, is a very dynamic process.
Since location of FtsZ ring was random in E. coli JM109∆minCD, the elongated cell needed more than two FtsZ rings in order to realize the multiple division. As the correct FtsZ concentration is required for the formation of FtsZ ring, plasmid (p15a-ftsZ) was constructed to regulate the expression level of ftsZ under the control of arabinose (Fig. 3). E. coli JM109ΔminCD harboring plasmid p15a-ftsZ was added with 0.2 % arabinose, E. coli JM109ΔminCD and E. coli JM109 harboring plasmid p15a-blank were used as control. After 2 h inoculation, E. coli JM109∆minCD (p15a-ftsZ) showed longer cell shape compared with the control groups (Figs. 4a, b, c). The length of E.coli JM109∆minCD was improved further by overexpression ftsZ, and the reason may be that the high expression level of FtsZ disrupted the normal division.

Over-expressing genes ftsQ, ftsL, ftsW and ftsN in E. coli JM109∆minCD improved the PHB contents
To enhance the growth of E. coli JM109∆minCD, the formation of FtsZ ring should be accelerated to reduce time spent for the cell division (or cell fission) process. Among many essential genes related to the division process, some have showed important functions, including ftsQ, ftsL, ftsW and ftsN. FtsZ interacts with these genes encoded proteins to complete cytokinesis [12,41].
Escherichia coli JM109ΔminCD harboring plasmid p15a-Pbad-ftsQLWN was added with 0.2 % arabinose after 2 h inoculation. And E. coli JM109ΔminCD with plasmid p15a-Pglta-ftsQLWN was added with 20 g/L glucose without arabinose. After cultured in LB medium for 48 h, E. coli JM109ΔminCD (p15a-Pglta-ftsQLWN) could reach 9.77 g/L cell dry weights containing 66.83 % PHB which was also higher than the control accumulating less than 60 % PHB (Fig. 5e). On the other hand, E. coli JM109ΔminCD (p15a-Pbad-ftsQLWN, pBHR68) grew to 11.39 g/L containing 70.06 % PHB, significantly higher than the control group (Fig. 5f ). It was therefore concluded that the cell dry weights and PHB contents were improved by overexpressing the division proteins in the multiple fission E. coli JM109∆minCD, the fast assembly of divisome complex could help the minCD mutant to accumulate more PHB granules. Furthermore, the cell dry weights and PHB contents were both higher in the mutant harboring plasmid p15a-Pbad-ftsQLWN than in the plasmid p15a-Pglta-ftsQLWN, indicating that an inducible promoter was better for PHB production. Since the mini-cells formed during the division process waste time and energy reducing space for PHB accumulation, it would be much better if the sizes of the mini-cells can become larger to be a viable cell. It has been known that enzyme complexes responsible for synthesizing cell elongation specific peptidoglycan are organized by the actin homolog MreB [35,42].
Escherichia coli changes to spherical shape from rod shape when the expression level of mreB changed. By overexpressing mreB, sizes of E. coli JM109∆minCD became larger than that of the control and wild types (Fig. 6a, b, c). When over-expressing mreB and PHB synthesis operon phbCAB encoded in plasmid pBHR68, E. coli JM109∆minCD (ptk-mreB, pBHR68) grew to 10.55 g/L containing 70.51 % PHB in the cell dry weights, significantly higher than the wild type grown to 9.11 g/L containing 48.52 % PHB (Fig. 6d). E. coli JM109∆minCD (ptk-mreB,pBHR68) showed longer and larger sizes (accompanied by many larger mini-cells) compared with the wild type, showing more PHB granule accumulation.
Sizes of mini-cells were also improved significantly, permitting more storage of PHB granules.

Over-expressing genes ftsQLWN and ftsZ together with scaffold gene mreB in E. coli JM109∆minCD increased cell growth and PHB production
The overexpression of FtsZ could speed up the formation of FtsZ ring, while FtsZ ring related genes ftsQ, ftsL, ftsW and ftsN (ftsQLWN) could accelerate the division process, additional manipulation of mreB could enlarge the cell size for more PHB granules accumulation. It was expected that the growth rate of E. coli JM109∆minCD could be enhanced if all the above genes were functionally expressed.
Escherichia coli JM109∆minCD (pBBR-Pbad-ftsQLWN, ptk-mreB-ftsZ) was then cultivated in LB medium without extra glucose. 20 mL culture broth was sampled regularly during the growth process for CDW. Arabinose was added to the cultures 2 and 4 h after inoculation, respectively. When Z-ring related genes ftsQLWN and ftsZ were over-expressed at the early stage of growth, the recombinant grew faster to reach 2.8 g/L, higher than 2.2 g/L of the control (Fig. 7b). However, cell growth was not enhanced more when arabinose induction was conducted 4 h after inoculation (Additional file 2: Figure S2). It seemed that gene overexpression in the early stage of cell growth had better effect on cell growth. Thus, arabinose induction was initiated after 2 h of inoculation in subsequent studies.
When over-expressing ftsQLWN, ftsZ and mreB together in the recombinant strain, E. coli JM109∆minCD (pBBR-Pbad-ftsQLWN, ptk-mreB-ftsZ, pBHR68) produced 82.13 % PHB in 11.58 g/L CDW, this means a one fold increase in PHB production over the control group (Fig. 7c). It was concluded that overexpression of these six genes together could increase the cell growth rate together with a significant increase on PHB accumulation.
Cell morphologies of recombinants E. coli JM109∆minCD overexpressing the six genes and PHB synthesis operon were studied under both SEM and TEM (Fig. 7d, e, f, g). It was observed that JM109∆minCD (pBBR-Pbad-ftsQLWN, ptk-mreB-ftsZ, pBHR68) was much larger than the control E. coli JM109 (pBBR1-MCS1, ptk-blank, pBHR68) (Fig. 7d, e). It was clearly observed that over expression on FtsZ ring and mreB genes resulted not only in large cell sizes but also in cells of various morphologies, which could be attributed to the unequal multiple fissions of the cells. The recombinant strain showed more PHB granule accumulation compared with the control group (Fig. 7f, g).

Discussion
In E. coli, the FtsZ ring at mid-cell ensures the binary fission, and the genes encoding proteins MinC and MinD inhibit formation of the FtsZ ring. As a result, overexpression of MinC and MinD in E. coli has been known to generate filament cells without FtsZ rings [19]. In contrast, the absence of MinC and/or MinD allows Z rings be formed in any position of a cell either at polar or medial positions [5]. The division pattern of E. coli JM109∆minCD changed from binary division to multiple fission, and uneven divisions resulted in some larger cells and some normal or smaller size cells. The influence on cell growth rate was limited by E. coli JM109∆minCD, however, the ability to produce PHB was enhanced, which could be attributed to the long cells generated from the multiple fission possessing more spaces for PHB granule storage, while wild type cells usually have equal small cell sizes.
Since FtsZ ring is important in cell division process, the concentration of FtsZ affects the cell morphology and cell division pattern as reported previously [39]. The length of E. coli JM109∆minCD was enhanced further by overexpressing ftsZ. PHB accumulation in JM109∆minCD (p15a-ftsZ) was elevated and the reason may be attributed to the long shape cell morphology. The high expression level of FtsZ could make cell longer which helped bacterial to store more inclusion bodies, but had little effect on cell growth rate.
In order to enhance the growth rate of E. coli JM109∆minCD, the division speed should be accelerated. After the formation of FtsZ ring, many genes showed important functions in assembly of the septal ring components, including ftsQ, ftsL, ftsW and ftsN [12,41]. We investigated the function of these four genes together. The cell growth rate had improved a little when overexpress ftsQ, ftsL, ftsW and ftsN genes together in E. coli JM109∆minCD, and the shake flask results demonstrated that the PHB production ability of E. coli JM109ΔminCD (p15a-Pbad-ftsQLWN, pBHR68) was enhanced significantly. The reason may be attributed to the longer cells with more Z rings of the overexpressing mutant, which could be divided into many daughter cells immediately as soon as the multiple FtsZ rings were formed. Due to the formations of many mini-cells during this multiple fission process, which did not contribute to the cell growth and PHB accumulation as mini-cells had no nucleic acid, the reduction on formations of mini-cells, by overexpression Fig. 7 The six genes co-expression system and the influence on cell morphology, PHA production. a The co-expression of six genes in E. coli JM109 ∆minCD. The pathway presented in a was the order of functional proteins in the division process. FtsA and ZipA bind directly to FtsZ polymers at the division site, followed by the sequential addition of FtsK, FtsQ, FtsL, FtsW, FtsI and FtsN. b The cell growth CDW by E. coli JM109 ∆minCD containing plasmid pBBR-Pbad-ftsQLWN and ptk-mreB-ftsZ, the arabinose was added to the culture after 2 h of inoculation. The control was cultivated under the same condition. Error bars are s.d. (n = 3). c The cell dry weight and PHA contents by the recombinant strain. The strains were grown in the LB medium at 30 °C to an OD600 = 0.4-0.6, followed by induction with 0.2 % arabinose for 6 h, then addition of 20 g/L glucose. Error bars are s.d. (n = 3). The SEM results of strains E. coli JM109 (pBBR1-MCS1, ptk-blank,pBHR68) (d) and E. coli JM109 ∆minCD(pBBR-Pbad-ftsQLWN,ptk-mreB,pBHR68) (e), Scale bars,10 μm. The TEM of PHB accumulation in E. coli JM109 (pBBR1-MCS1, ptk-blank,pBHR68) (f) and E. coli JM109 ∆minCD (pBBR-Pbad-ftsQLWN,ptk-mreB,pBHR68) (g), Scale bars, 2 μm. (d-g) All the strains were grown in the LB medium at 30 °C to an OD600 = 0.4-0.6, followed by induction with 0.2 % arabinose for 6 h, then addition of 20 g/L glucose for another 40 h of cultivation division protein, may be able to improve both cell growth and PHB accumulations.
Since the mini-cells formed during the division process waste time and energy reducing space for PHB accumulation, it would be much better if the sizes of the minicells can become larger to be a viable cell. It has been known that enzyme complexes responsible for synthesizing cell elongation specific peptidoglycan are organized by the actin homolog MreB [35]. When overexpressing mreB in E. coli JM109∆minCD, the width of the cell was enhanced and size was bigger compared with wild type, especially within PHB granules. As a result, the ability of PHB production was enhanced by E. coli JM109ΔminCD overexpressing mreB.
As the ftsZ and ftsQLWN genes could enhance the cell length, and mreB gene could enhance the cell width, we constructed two plasmids expressing the six genes together in E. coli JM109∆minCD. The cell growth rate was accelerated under the function of the high expression level of the six genes. Furthermore, the size of the cell was bigger than the wild type, and the big volume could contain more PHB. The PHB production ability of JM109∆minCD (pBBR-Pbad-ftsQLWN, ptk-mreB-ftsZ) was elevated significantly. In conclusion, multiple division and larger cell morphology could enhance the storage space in the cells, and we provide new insights into the PHB production mechanism.
Compared with other efforts to improve PHB production, such as process optimization and PHB pathway engineering et al., the multiple division and larger cell morphology could enhance the production further and provide a new vision on improved PHB production. In order to satisfy the industrialization purpose, there are still many further engineering solutions needed in the new system, such as the improvement on stability of recombinant strain, the reduction of time spending on bacterial division. The work on division pattern and cell morphology of E. coli can help improve cell factories more efficiently.

Conclusions
Bacterial cells are grown in a binary fission way meaning a bacterial cell is equally divided into two (1-2 division). This common growth pattern of E. coli can be changed to multiple fission patterns (1 to n, n > 2) by deleting fission related genes minC and minD together or individually, allowing the formation of multiple fission rings (FtsZ-rings) in several positions of an elongated E. coli cell. However, even though a bacterial cell was able to divide into more than two daughter cells, we could not observe significant faster cell growth. To further improve cell growth, some genes related to the divison including ftsQ, ftsW, ftsN, ftsL and ftsZ, together with the cell shape control gene mreB, were all overexpressed in E. coli JM109∆minCD. Different degrees of cell growth changes were visible. The changing pattern of E. coli cell growth resulted in more cell dry weights (CDW) and more than 80 % PHB accumulation increases compared to its binary fission control grown under the same conditions. This study clearly demonstrated that the disrupted min system can change the cell division pattern from binary to multiple fission. Combined over-expression of Z ring synthesis genes ftsQ, ftsW, ftsN, ftsL and ftsZ together with shape control gene mreB led to enhanced PHB accumulation.

Bacterial strains, plasmids and culture conditions
All the microorganisms and plasmids used in this study are listed in Table 2. E. coli strains were cultivated in Luria-Bertani (LB) medium or mineral medium (MM). LB medium contains (g/L) 10 tryptone, 5 yeast extract and 10 NaCl. MM medium consists of (g/L): (NH4) 2  and HCl 0.5 M. When antibiotic selection pressure was required, the medium was supplemented with ampicillin (100 μg/mL), kanamycin (50 μg/mL) or chloramphenicol (30 μg/mL). In order to produce PHA by E. coli, 20 g/L glucose was added into the culture medium as a carbon source.

Construction of plasmids and recombinant strains
Molecular cloning standard procedures including DNA amplification, restriction enzyme digestion and other DNA manipulations were employed for plasmids construction [43]. The kits of DNA purification, plasmids isolation and ligation were purchased from Biomed (Beijing, China) and Thermo (Beijing, China). Primers used in this study were all synthesized by Invitrogen Company (Shanghai, China). In order to construct larger plasmid, the Gibson assembly kit was used in this work (NEB, China) [44].

Genes minC and minD knockout in E. coli
Escherichia coli JM109ΔminCD mutant was constructed by one-step disruption on the chromosome [45]. 500 bp homologous upstream and downstream of target gene DNA, and the Kan R gene flanked by FLP recognition target (FRT) sites from plasmid pKD13, were used to form the deletion fragment by PCR amplification. The primers used in this study are listed in Additional file 3: Table S1.