The complete genome sequence ofChromobacterium violaceumreveals remarkable and exploitable bacterial adaptability

Abstract

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) Ϸ500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) widespread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications.T he genomes of soil-and water-borne free-living bacteria have received relatively little attention thus far in comparison to pathogenic and extremophilic organisms, yet they provide fundamental insights into environmental adaptation strategies and represent a rich source of genes with biotechnological potential and medical utility. A particularly interesting organism of this kind is Chromobacterium violaceum, a Gram-negative ␤-proteobacterium first described at the end of the 19th century (1), which dominates a variety of ecosystems in tropical and subtropical regions. This bacterium has been found to be highly abundant in the water and borders of the Negro river, a major component of the Brazilian Amazon (2) and as a result has been studied in Brazil over the last three decades. These, in general, have focused on the most notable product of the bacterium, the violacein pigment, which has already been introduced as a therapeutic compound for dermatological purposes (3). Violacein also exhibits antimicrobial activity against the important tropical pathogens Mycobacterium tuberculosis (4), Trypanosoma cruzi (5), and Leishmania sp. (6) and is reported to have other bactericidal (2, 7-10), antiviral (11), and anticancer (12, 13) activities.Some other aspects of the biotechnological potential of C. violaceum have also begun to be explored, including the synthesis of poly(3-hydroxyvaleric acid) homopolyester and other shortchain polyhydroxyalkanoates, which might represent alternatives to plastics derived from petrochemicals (14, 15), the hydrolysis of plastic films (16), and the solubilization of gold through a mercury-free process, thereby avoiding environmental contamination (17, 18). These studies, however, have been based on knowledge of only a tiny fraction of the genetic constitution of the organism. In addition, the more basic issues of the mechanisms and strategies underlying the adaptability of C. violaceum, including its observed but infrequent infection of h...

Global Transcriptional Response to Organic Hydroperoxide and the Role of OhrR in the Control of Virulence Traits in Chromobacterium violaceum

“…S2), confirming previously reported data (17). After a detailed inspection of data in the NCBI Reference Sequence (RefSeq) database, we realized that the CV_0208 gene is larger than previously annotated (21) (Fig. 5A).…”

“…As a saprophytic microorganism, this Gram-negative bacterium encounters natural and xenobiotic aromatic compounds present in soils and is potentially able to use them as carbon sources or deal with their toxic effects (21,22). The aromatic peroxide CHP can be released in these environments as an intermediate product from lignin catabolism (23) or as a pollutant derived from the chemical industry (24).…”

Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1

“…Moreover, based on gene assignments to the “Energy Metabolism” functional role category of The Institute for Genomic Research (TIGR) (http://cmr.tigr.org/tigr-scripts/CMR/RoleIds.cgi), 17.7% of the TC1 genome (833 ORFs) is devoted to energy production. This is in contrast to many sequenced organisms in which approximately 4%–7% of genes are involved in energy production and conversion [42]. Consistent with the extensive metabolic versatility associated with the degradation of s -triazines and other compounds, TC1 encodes 568 putative transporters and binding proteins (12.06% of the TC1 genome): 101 for amines, peptides, and amino acids, and 107 for carbohydrates, alcohols, and acids.…”

Identification and Characterization of the Sulfazecin Monobactam Biosynthetic Gene Cluster

“…Since its discovery in the early 1980s in the producing strain Pseudomonas acidophila (Asai et al, 1981), however, very little research has been conducted on its molecular origin (Parker et al, 1986). The genomes of a few species related to monobactam producers have been fully sequenced (Brazilian National Genome Project Consortium, 2003). However, searching for isopenicillin synthetase (Leskiw et al, 1988) or β-lactam synthetase (Bachmann et al, 1998) paralogs resulted in no hits.…”