Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems

Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given

Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems

Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given

Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems

Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given

Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems

Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html. The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in CuA assembly in more than a thousand prokaryotes

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html. The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in CuA assembly in more than a thousand prokaryotes

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html. The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in CuA assembly in more than a thousand prokaryotes

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html. The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in CuA assembly in more than a thousand prokaryotes

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html. The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in CuA assembly in more than a thousand prokaryotes