Extra work

Crusher of molecules inside the cells also creates proteins that reduce the efficiency of vaccines

eduardo cesarRepresentation of splicing: new proteins with patches of the old oneseduardo cesar

Nature keeps giving examples that it can be more complicated than it seems. Two recent articles, one published in Nature and the other in Science, reveal a phenomenon that is making a little more difficult the already troubled life of the researchers who are studying proteins – in Brazil, there are about 300 groups dedicated to this area. Around the nucleus of the cell, in the portion called cytoplasm, there is a cylindrical structure, made up of proteins, that acts like a crusher, getting rid of the old and defective proteins in its units, the amino acids.

It used to be thought that these amino acids became free and were put to further use in the production of new proteins – which form cells and tissues, in short the organism of plants and animals – only in another cell compartment, the ribosome, following recipes contained in the genetic material of the cells, the molecule of deoxyribonucleic acid (DNA). What is now appearing clearly is that the proteins responsible for this dismantling are also capable of forming other proteins. This parallel production, identified this year, shows that the proteins previously believed to be capable only of cutting out other proteins completely are not doing the full job. Some of them, besides cutting up, also regroup distant stretches of the partially dismantled protein, modifying it before going into action.

The recombination or splicing of proteins, as the recently discovered process is called, helps us to understand why some vaccines do not work as they ought to. The vaccines are made from antigens, or fragments of proteins that activate the defense cells and prepare the organism for facing up to the viruses and bacteria that produce them. But as the set of possibilities for recombination of stretches of proteins is ample, antigens may appear against which organism is not prepared. “This mechanism exercises a clear influence on antigens, whose diversity should increase significantly”, Ricardo Zorzetto, from Pesquisa FAPESP, was told by Benoît Van den Eynde, from the Ludwig Cancer Research Institute, in Brussels, Belgium, the coordinator of the study published on-line by Science on March 4 and shown in the printed version of the magazine on April 23.

“This is certainly not a rare phenomenon, since two other examples have now been described since the publication of our article”, James Yang told Pesquisa FAPESP, from the National Cancer Institute (NCI), of the United States, the first to identify this mechanism in the human organism. After his study, carried out with kidney tumor cells and announced on January 15 in Nature, this alternative form for producing proteins was observed by Van den Eynde’s team in skin tumor cells and by another group of researchers from the NCI, in a study to be published shortly.

Described almost 20 years ago in plant cells, and later in unicellular organisms, only now has the slicing of proteins been observed in animals. It is a discovery that helps to explain why the human organism produces about 90,000 different proteins, although it has only some 30,000 recipes registered in the DNA. But, for the time being, the identification of the splicing of proteins creates more doubts than answers, claims immunologist Hans-Georg Rammensee, from the University of Tübingen, Germany, in a comment on Yang’s work, also published in Nature in January.

Rule or exception?
“We do not know yet whether, in mammals, the peptides (protein fragments) produced in this way have a different function [from those made from the DNA]”, Yang recognized. Even so, Rammensee points out another possible consequence of the recently described mechanism: although it is not know how frequent is the production of proteins from the breaking down of an original molecule and the rewelding of its parts, the possibility exists that this recombination occurs not only with proteins of tumor cells, but also with proteins of normal cells of viruses and bacteria that infect the organism, making it more difficult to get vaccines against some diseases.

The discovery of this mechanism suggests that the exceptions to the model created 40 years ago – the production of proteins solely from the DNA – are more common than one might imagine. A clue to the complexity of the manufacture of proteins arose more than two decades ago, with the identification of the splicing of RNA. Copied from the DNA, the molecule of RNA, or ribonucleic acid, transports the recipe for producing proteins from the nucleus to the cytoplasm. On the way, it may lose some of its internal segments. As a result, the protein made under the command of this shortened RNA could not have been anticipated only by the examination of the stretch of the DNA that originated it.

It was by chance that Yang arrived at the splicing of proteins. A few years ago, he found that T-lymphocytes, a kind of cell from the immune system, were very active in a person with kidney cancer. The T-lymphocytes recognized a fragment of a protein manufactured in high quantities by the cancer cells, the fibroblast growth factor 5 (FGF-5). With the aim of arriving at a medicine against tumors, Yang decided to investigate which amino acids made up this fragment of the FGF-5. He found that this stretch was the result of the breaking up and random reorganization of the molecule after it was ready: from a segment of 49 amino acids, 40 amino acids from the intermediate portion were excluded, and five from one end were united to four from the other.

Researchers from the Ludwig Institute, in Brussels, and from the University of Liège, also in Belgium, concluded that this recombination occurs in the protein crusher ? the proteasome. Van den Eynde observed this phenomenon when studying a fragment – peptide – derived from an antigen produced by cells of melanoma, the most aggressive of skin cancers. After they are ready, only one in every 10,000 peptides undergoes splicing, which makes use of the energy generated in the very breaking up of the proteins discarded by the organism.