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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0133

PubMed

15671160, Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):3906-12. doi: 10.1073/pnas.0409188102. Epub 2005 Jan 25.

Characterization method

sequence homology analysis

Genomic accession number

CP000033.3

Nucelotide position range

1759462-1771472

Substrate

exopolysaccharide

Loci

LBA1724-LBA1737

Species

Lactobacillus acidophilus/1579

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

epsI LBA1724 AAV43536.1 0 - 1434 (-) CP000033.3:1759462-1760896 -
epsJ LBA1725 AAV43537.1 1439 - 1966 (-) CP000033.3:1760901-1761428 5.4.99.9
- LBA1726 AAV43538.1 2150 - 2552 (-) CP000033.3:1761612-1762014 5.4.99.9
- LBA1727 AAV43539.1 2548 - 3844 (-) CP000033.3:1762010-1763306 -
- LBA1728 AAV43540.1 3868 - 4909 (-) CP000033.3:1763330-1764371 -
- LBA1729 AAV43541.1 4905 - 5562 (-) CP000033.3:1764367-1765024 -
- LBA1730 AAV43542.1 5530 - 6064 (-) CP000033.3:1764992-1765526 -
- LBA1731 AAV43543.1 6064 - 6960 (-) CP000033.3:1765526-1766422 -
epsF LBA1732 AAV43544.1 6962 - 7748 (-) CP000033.3:1766424-1767210 -
epsE LBA1733 AAV43545.1 7744 - 8413 (-) CP000033.3:1767206-1767875 -
epsD LBA1734 AAV43546.1 8487 - 9258 (-) CP000033.3:1767949-1768720 -
epsC LBA1735 AAV43547.1 9260 - 10054 (-) CP000033.3:1768722-1769516 -
epsB LBA1736 AAV43548.1 10058 - 10945 (-) CP000033.3:1769520-1770407 -
epsA LBA1737 AAV43549.1 10955 - 12011 (-) CP000033.3:1770417-1771473 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

epsI 1 - 1434 (-) TC: gnl|TC-DB|Q8KUK6|2.A.66.2.16 Yes
epsJ 1440 - 1952 (-) other Yes
- 2151 - 2552 (-) STP: STP|Pyr_redox Yes
- 2549 - 3844 (-) other Yes
- 3869 - 4909 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 4906 - 5562 (-) other Yes
- 5531 - 6052 (-) other Yes
- 6065 - 6946 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
epsF 6963 - 7736 (-) other Yes
epsE 7745 - 8398 (-) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes
epsD 8488 - 9258 (-) other Yes
epsC 9261 - 10043 (-) TC: gnl|TC-DB|P39851|8.A.3.2.1 Yes
epsB 10059 - 10934 (-) TC: gnl|TC-DB|P72367|8.A.3.2.4 Yes
epsA 10956 - 12011 (-) CDS No

PUL ID

PUL0133

PubMed

15671160, Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):3906-12. doi: 10.1073/pnas.0409188102. Epub 2005 Jan 25.

Title

Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.

Author

Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M, Lick S, Hamrick A, Cano R, Klaenhammer TR

Abstract

Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.