The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability Brazilian National Genome Project Consortium*

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 gen-eration, (ii) Ϸ500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread 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, pos-sibly 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 includ-ing 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 funda-mental insights into environmental adaptation strategies and rep-resent 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 short-chain 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 contam-ination (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 mecha-nisms and strategies underlying the adaptability of C. violaceum, including its observed but infrequent infection of humans, have not been deeply investigated at the molecular and genetic levels. To begin to rectify the paucity of our basic knowledge of this remarkable organism we sequenced and annotated the complete genome of C. violaceum type strain ATCC 12472. This has revealed a detailed portrait of the molecular complexity required for the organism's versatility as well as an extended compendium of ORFs that significantly increase the biotechnological poten-tial of the bacterium.