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Table 1 Conserved domains of enzymes for biosynthesis and depolymerization of polyhydroxyalkanoate of Bacillus species.

From: Bacillus subtilis as potential producer for polyhydroxyalkanoates

Description

β-Keto thiolase

Acetoacetyl reductase

Polyhydroxyalkanoate

    

Synthase

Depolymerase

 

PhaA

PhaB

 

PhaC

PhaR

PhaZ

 

Thiolase

NADB

FabG

PhaC

PRK

03918

DepA

Bacillus cereus 03BB102

Fa

F

F

F

Pb

F

B. cereus 03BB108

F

F

F

F

P

F

B. cereus AH1134

F

F

F

F

Ac

F

B. cereus AH187

F

F

F

F

P

F

B. cereus AH820

F

F

F

F

P

F

B. cereus ATCC 10987

F

F

F

F

P

F

B. cereus ATCC 14579

F

F

F

F

A

F

B. cereus B4264

F

F

F

F

A

F

B. cereus E33L

F

F

F

F

P

F

B. cereus G9241

F

F

F

F

P

F

B. cereus G9842

F

F

F

F

A

F

B. cereus H3081.97

F

F

F

F

P

F

B. cereus NVH0597-99

F

F

F

F

P

F

B. cereus Q1

F

F

F

F

P

F

B. cereus subsp. cytotoxis NVH 391–98

F

F

F

F

A

F

B. cereus W

F

F

F

F

P

F

B. thuringiensis serovar israelensis ATCC 35646

F

F

F

F

A

F

B. thuringiensis serovar konkukian str. 97-27

F

F

F

F

P

F

B. thuringiensis str. Al Hakam

F

F

F

F

P

F

B. anthracis str. A0193

n/ad

F

F

F

P

F

B. anthracis str. A0389

n/a

F

F

F

P

F

B. anthracis str. A0442

n/a

F

F

F

P

F

B. anthracis str. A0465

n/a

F

F

F

P

F

B. anthracis str. A0488

n/a

F

F

F

P

F

B. anthracis str. A2012

F

F

F

F

n/a

F

B. anthracis str. Ames

F

F

F

F

P

F

B. anthracis str. 'Ames Ancestor'

F

F

F

F

P

F

B. anthracis str. Sterne

F

F

F

F

P

F

B. coagulans 36D1

F

F

F

A

A

A

B. coahuilensis m4-4

F

F

F

F

A

F

B. weihenstephanensis KBAB4

F

F

F

F

A

F

B. amyloliquefaciens FZB42

F

n/a

n/a

n/a

n/a

n/a

B. subtilis subsp. subtilis str. JH642

n/a

n/a

n/a

n/a

n/a

n/a

B. subtilis

subsp. subtilis str. SMY

F

F

F

n/a

n/a

n/a

B. subtilis subsp. subtilis str. 168

n/a

Fe

Fe

n/a

n/a

n/a

B. subtilis

subsp. subtilis str. NCIB 3610

F

F

F

A

A

F

B. licheniformis

F

F

F

n/a

n/a

n/a

B. licheniformis ATCC 14580

F

F

F

n/a

n/a

n/a

B. pumilus ATCC 7061

F

F

F

A

A

A

B. pumilus SAFR-032

F

F

F

A

A

A

B. halodurans C-125

F

F

F

A

A

A

B. clausii KSM-K16

F

F

F

A

A

A

B. megaterium

n/a

F

F

F

A

F

B. selenitireducens MLS10

F

F

F

A

A

A

Bacillus sp. B14905

F

F

F

A

A

A

Bacillus sp. C18

n/tf

n/t

n/t

F

n/t

P

Bacillus sp. C19

n/t

n/t

n/t

P

n/t

P

Bacillus sp. E13

n/t

n/t

n/t

P

n/t

P

Bacillus sp. INT005

na

F

F

F

P

F

Bacillus sp. NRRL B-14911

F

F

F

F

A

A

Bacillus sp. SG-1

F

F

F

A

A

A

  1. a: Full domain present
  2. b: Partial domain present
  3. c: Domain absent
  4. d: Not applicable
  5. e: Enzyme was β-ketoacyl-acyl carrier protein reductase and the gene was fabG
  6. f: Not traceable (due to partial sequencing)
  7. Sequence analysis and pathway alignment of polyhydroxyalkanoate metabolism was done as described earlier [71]. Screening of Bacillus spp. in KEGG (Kyoto Encyclopedia of Genes and Genomes) http://www.genome.ad.jp database was performed for PHA biosynthesis enzymes β-ketoacyl-CoA thiolase (PhaA-EC 2.3.1.9), an NADPH dependent Acetoacetyl-CoA reductase (PhaB-EC 1.1.1.36) and PHA synthase (PhaC-EC 2.3.1.41). The conserved domains for these enzymes were identified from RPS-BLAST [71] (reverse position-specific – basic local alignment search tool) at National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov. Amino acid sequences of PhaA (GenBank accession no. AAP11875), PhaB (GenBank accession no. AAP08300), and PhaC (including PhaZ) (GenBank accession no. AAP08301) of Bacillus cereus ATCC 14579, and PhaR (GenBank Accession no.: AAD05258) of B. megaterium were used as a queries against the Bacillus sequenced genome database using BLAST.